Code

Docs update#265

Code

Merged

bgyori merged 77 commits intomaingyorilab/mira:mainfrom docs-updategyorilab/mira:docs-updateCopy head branch name to clipboardDec 7, 2023

+2,983-664

Commits

Commits on Dec 6, 2023

• Fix underlines in modeling.rst

  kkaris

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  50ba081

• Fix underlines in sources.rst

  kkaris

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  e092c73

• Fix typo

  kkaris

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  c3f0164

• Add sources/decapodes to docs

  kkaris

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  0bad74b

• Extend docstrings for terarium client functions

  kkaris

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  9847599

• Fix title underline

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  a221ce5

• Add docstring to sanity_check_amr

  kkaris

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  628039f

• Fix ValueError message

  kkaris

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  cadcc30

• Add file header to sources/amr/regnet.py

  kkaris

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  f760662

• Extend docstring for stock_to_concept in sources/amr/stockflow.py

  kkaris

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  3abec4b

• Extend docstring for reproduce_ode_semantics

  kkaris

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  d1bb8d6

• Extend docstrings in sources/sbml/api.py

  kkaris

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  ed116a3

• Add utility file to sources.rst and add docstrings to methods in sources module

  

  nanglo123

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  kkaris

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  18f61e5

• Add description to search query text

  kkaris

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  085956f

• Fix URL in description

  kkaris

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  7724b40

• Fix more links

  kkaris

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  308effd

• Add description for entity_similarities arg

  kkaris

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  9358ba3

• Add example in response to /is_ontological_child

  kkaris

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  c4d7263

• Delete ignored title

  kkaris

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  236ff08

• Use functools wraps to expose docstrings

  kkaris

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  39df6dd

• Add file docstring

  kkaris

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  25264f9

• Add Concept to __all__ in template_model.py

  kkaris

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  1ff58c6

• Clean up docstring for add_transition()

  kkaris

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  4847d3f

• Rename argument in wrapper to correspond to docstrings

  kkaris

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  cd2bd3e

• Add/extend docstrings for functions in modeling/amr/ops.py

  kkaris

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  f26950f

• Copy over docstrings for pure wrapping of functions

  kkaris

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  ddf9dd7

• Update metamodel/decapodes, metamodel/template_model and modeling/acsets/stockflow

  

  nanglo123

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  kkaris

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  070ca2b

• Do some fixing of wrapped docstrings in pure wrappers

  kkaris

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  5255594

• Explicitly import classes/methods from modules for tests and revert changes to docstrings for template_model class such that tests pass

  

  nanglo123

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  kkaris

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  5bd8f80

• Fix undeline

  kkaris

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  d2fed22

• Add docstrings to template_model.py, update schema, fix error message for schema test

  

  nanglo123

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  kkaris

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  2299423

• Update template model schema

  

  nanglo123

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  kkaris

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  cc2edcf

• Extend docstring for query_biomodels in sources/biomodels.py

  kkaris

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  ca6fe6f

• Replace json typing with generic JSON

  kkaris

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  5423565

• Extend docstrings in modeling/amr/petrinet.py

  kkaris

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  874ca9d

• Extend docstrings in modeling/amr/regnet.py

  kkaris

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  854ea4d

• Remove extra underlines

  kkaris

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  3d19174

• Extend docstrings in mira/modeling/bilayer.py

  kkaris

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  89fed1a

• Add docstrings to modeling/__init__.py

  kkaris

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  4b2c964

• Extend docstrings for metamodel/io.py

  kkaris

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  4e884a0

• Extend docstring of find_models_with_grounding in metamodel/search.py

  kkaris

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  17e05f2

• Add missing return section in io.py

  kkaris

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  b5c6db9

• Extend docstring for get_json_schema in schema.py

  kkaris

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  90bceb9

• Extend docstrings in metamodel/comparison.py

  kkaris

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  2adf331

• Fix warning in docs build

  kkaris

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  dcbca4c

• Extend docstrings in metamodel/ops.py

  kkaris

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  6dbd07b

• Extend some docstrings in metamodel/templates.py

  kkaris

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  6d86894

• Add more information to method docstrings in sources module

  

  nanglo123

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  kkaris

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  e86761a

• Add docstring for constructor of Decapode class

  

  nanglo123

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  kkaris

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  0ff6735

• add docstring to to_json method of modeling/acsets/stockflow

  

  nanglo123

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  kkaris

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  b696c87

• Update schema and improve docstring punctuation for template_model.py

  

  nanglo123

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  kkaris

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  46069f2

• Get schema using pydantic 1.10.13

  kkaris

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  6c844fb

• Finish the docstring extensions in templates.py

  kkaris

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  7259985

• Update schema.json again

  kkaris

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  3822397

• Fix file header

  kkaris

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  e79e97d

• Update file headers in chime.py and mech_bayes.py

  kkaris

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  6495df1

• Include examples module in docs

  kkaris

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  54a5758

• Link to directory in decapodes example README.md

  kkaris

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  b860df1

• Add/extend docstrings for helpers in decapodes_examples.py

  kkaris

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  38e1168

• Add example values to add_transition endpoint

  kkaris

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  9a3f120

• Add example to AMRComparisonQuery

  kkaris

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  271ce57

• Update contact visible in API docs

  kkaris

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  d1637da

• Add 4 different notebooks to README

  

  nanglo123

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  kkaris

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  34b264e

• Fix attribute docstrings for each dataclass to follow standard formatting in Decapodes class

  

  nanglo123

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  kkaris

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  590df6d

• Change dict to Dict in docstrings for util file in sources

  

  nanglo123

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  af9eef2

• Add spaces between colons for listed parameters in docstrings

  

  nanglo123

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  kkaris

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  e0ca2d8

• Fix wording of notebook 10 description in README

  

  nanglo123

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  kkaris

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  2e667b0

• Add typing to returned JSON

  

  nanglo123

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  kkaris

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  9e86543

• Fix typing for keys for input dictionaries to decapode class

  

  nanglo123

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  kkaris

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  719eb02

• Add spaces between colons and variables in docstrings and rewrite dict as Dict

  

  nanglo123

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  kkaris

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  22fe992

• Include more classes in templates module

  kkaris

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  d796b75

• Exclude main function in biomodels

  kkaris

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  08f7d88

• Remove unused parameter

  kkaris

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  3476814

• Add more spaces between : in docstring for methods in modeling/acsets/stockflow

  nanglo123

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  9545b0a

• Add subheading for mira.modeling

  kkaris

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  666ddd7

Commits on Dec 7, 2023

• Reflect same method docstring consistency across different modules

  nanglo123

  committed
  0ca3e41

• Remove type annotation for parameter

  nanglo123

  committed
  b7ef9f6